We study the dynamics of knotted vortices in a bulk excitable medium using the FitzHugh-Nagumo model. From a systematic survey of all knots of at most eight crossings we establish that the generic behavior is of unsteady, irregular dynamics, with prolonged periods of expansion of parts of the vortex. The mechanism for the length expansion is a long-range "wave-slapping" interaction, analogous to that responsible for the annihilation of small vortex rings by larger ones. We also show that there are stable vortex geometries for certain knots; in addition to the unknot, trefoil, and figure-eight knots reported previously, we have found stable examples of the Whitehead link and 6_{2} knot. We give a thorough characterization of their geometry and steady-state motion. For the unknot, trefoil, and figure-eight knots we greatly expand previous evidence that FitzHugh-Nagumo dynamics untangles initially complex geometries while preserving topology.
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http://dx.doi.org/10.1103/PhysRevE.99.012211 | DOI Listing |
J Chem Phys
May 2023
Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA.
We used Langevin dynamics simulations without hydrodynamic interactions to probe knot diffusion mechanisms and the time scales governing the evolution and the spontaneous untying of trefoil knots in nanochannel-confined DNA molecules in the extended de Gennes regime. The knot untying follows an "opening up process," wherein the initially tight knot continues growing and fluctuating in size as it moves toward the end of the DNA molecule before its annihilation at the chain end. The mean knot size increases significantly and sub-linearly with increasing chain contour length.
View Article and Find Full Text PDFJ R Soc Interface
April 2023
Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK.
Quantification and classification of protein structures, such as knotted proteins, often requires noise-free and complete data. Here, we develop a mathematical pipeline that systematically analyses protein structures. We showcase this geometric framework on proteins forming open-ended trefoil knots, and we demonstrate that the mathematical tool, persistent homology, faithfully represents their structural homology.
View Article and Find Full Text PDFJ Phys Chem B
December 2022
Division of Sciences and Mathematics, Interdisciplinary Arts and Sciences, University of Washington Tacoma, Tacoma, Washington98402, United States.
Formation of protein knots is an intriguing offshoot of the protein folding problem. Since experimental resolution on knot formation is limited, theoretical methods currently provide the most detailed insights into the knotting process. While suitable for shallow knots, molecular dynamics simulations have faced challenges capturing the formation of deep knots in proteins such as the minimally tied trefoil α/β methyltransferase from (MTT).
View Article and Find Full Text PDFPhys Chem Chem Phys
November 2022
Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing 100081, China.
The knotted proteins are a class of rare but biologically important proteins, due to the special topology of their native structure. Here we present a simple method to identify the key residues for knotting and unknotting in a knotted protein, using the trefoil protein MJ0366 as an example. We first simulate the folding process the annealing molecular dynamics (AMD) simulations in the coarse-grained "Go"-like model.
View Article and Find Full Text PDFNature
October 2021
Ginzton Laboratory and Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
Effects connected with the mathematical theory of knots emerge in many areas of science, from physics to biology. Recent theoretical work discovered that the braid group characterizes the topology of non-Hermitian periodic systems, where the complex band energies can braid in momentum space. However, such braids of complex-energy bands have not been realized or controlled experimentally.
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